相关论文: Reactive Vortexes in a Naturally Activated Process…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
Water mediates a broad range of chemical reactions, including proton transfer, bond rearrangement, and conventional radical processes, defining a continuously expanding repertoire of intrinsic reactivity. However, roaming, a fundamental…
To gain insight into reaction mechanism of activated processes, we introduce an exact approach for quantifying the topology of high-dimensional probability surfaces of the underlying dynamic processes. Instead of Morse indexes, we study the…
An activated process consists of energy activation and barrier crossing; the former is a prerequisite for the latter. Barrier crossing has been studied extensively, but energy activation has been overlooked due to a lack of means to gauge…
The efficiency of an encounter-controlled two-channel reaction between two independently-mobile reactants on a lattice is characterized by the mean number $\rt$ of steps to reaction. The two reactants are distinguished by their mass with…
Reaction-diffusion systems where transition rates exhibit quenched disorder are common in physical and chemical systems. We study pair reactions on a periodic two-dimensional lattice, including continuous deposition and spontaneous…
Stochasticity plays important roles in reaction systems. Vector fields of probability flux and velocity characterize time-varying and steady-state properties of these systems, including high probability paths, barriers, checkpoints among…
We examine the interactions between actively rotating proteins moving in a membrane. Experimental evidence suggests that such rotor proteins, like the ATP synthases of the inner mitochondrial membrane, can arrange themselves into lattices.…
In closed quantum systems, a dynamical phase transition is identified by nonanalytic behaviors of the return probability as a function of time. In this work, we study the nonunitary dynamics following quenches across exceptional points in a…
In this work we study the dynamical behavior of two interacting vortex pairs, each one of them consisting of two point vortices with opposite circulation in the 2d plane. The vortices are considered as effective particles and their…
The present work shows that the free energy landscape associated with alanine dipeptide isomerization can be effectively represented by specific interatomic distances without explicit reference to dihedral angles. Conventionally, two stable…
Diffusion-coagulation can be simply described by a dynamic where particles perform a random walk on a lattice and coalesce with probability unity when meeting on the same site. Such processes display non-equilibrium properties with strong…
A vortex molecule is a topological excitation in two coherently coupled superfluids consisting of a vortex in each superfluid connected by a domain wall of the relative phase, also known as a Josephson vortex. We investigate the dynamics of…
We examine a two-dimensional system of sterically repulsive interacting disks where each particle runs in a random direction. This system is equivalent to a run-and-tumble dynamics system in the limit where the run time is infinite. At low…
Active turbulence, or chaotic self-organized collective motion, is often observed in concentrated suspensions of motile bacteria and other systems of self-propelled interacting agents. To date, there is no fundamental understanding of how…
To describe vibrationally mediated configuration changes of adsorbates on surfaces we have developed a new theory to calculate both reaction rates and pathways. The method uses the T-matrix to describe excitations of vibrational states by…
A major impediment to a more complete understanding of barrier crossing and other single-molecule processes is the inability to directly visualize the trajectories and dynamics of atoms and molecules in reactions. Rather, the kinetics are…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
Systems switching between different dynamical phases is an ubiquitous phenomenon. The general understanding of such a process is limited. To this end, we present a general expression that captures fluctuations of a system exhibiting a…
A model Hamiltonian for the reaction CH$_4^+ \rightarrow$ CH$_3^+$ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose…